Evolving Bonds
by pain17ification
Summary: During Naruto and Jiraiya's trip, they make one last stop to the city of Altomare! There, Naruto discovers a species the Elemental Nations have never even heard of and bonds with a certain red eon! See what happens when she decides to go to the Elemental Nations with him and what surprises lay in wait for Naruto upon his return! Pokémon aren't the only things that evolve, y'know!
1. Chapter 1: Birth of a Bond

Hello FanFiction! This is pain17ification with a Naruto/Pokémon Xover! Wish me luck and I hope you enjoy the idea!

Please Note: Due to difficulty trying to make PokéMoves typed in Japanese, all techniques (both chakra and PP based) will be portrayed in English!

Disclaimer (aka: pain in the ass): pain17ification doesn't own anything except for the story idea

"Speech"

'_Thoughts'_

**Techniques**

_**Bijuu**_

_Radio/TV_

_"Telepathic"_

[Scene Shift]

**Chapter 1: Birth of a Bond**

"Damn pervert, leaving me alone in a big city like this," muttered an angry male as he trekked through the beautiful streets of the port city of Altomare, far from the Elemental Nations.

He was a man of about 18yrs of age and quite tall with his even 6ft frame. From the bottom up he wore black boot-like sandals that left his toes and heel visible, dark gray cargo pants with a white belt holding both them and his pouch up, and a black long sleeved shirt that had the cuffs and collar colored in an orange trim along with a red swirl on the back. Around his neck was a string necklace with a green gem resting over his chest while an orange cloth with a metal plate was wrapped around his left bicep. The plate had a leaf like symbol with a spiraling center on it, showing just where he came from.

His face had the faintest bit of baby fat left if you looked hard enough, though it would be hard to spot since most people where drawn to his cheeks. On each one were three line markings that looked to be whiskers similar to that of a feline or canine. Piercing blue eyes as deep as the ocean waves were visible just under the fringe caused by his bright red hair. Said hair was wild, untamed, and slightly bushy as it extended past his head from behind down to his mid back while his fringe fell to between his eyes and twin bangs framed his face. (1)

This man was Naruto Uzumaki, a Genin from the Leaf Village of the Elemental Nations. He and his master, Jiraiya of the Sannin, were making one of their final stops of their three year training trip. So far, the trip had been fairly successful in the man's opinion. He had refined what many called an excuse of a taijutsu, learned of the many ways to dispel genjutsu, learned of his chakra nature and some jutsu for it, perfected the Fourth's signature jutsu, and was blazing through fuinjutsu studies.

Of all the subjects they touched on, fuinjutsu was by far the one that raked in the most progress. It came naturally to him – as soon as his handwriting and calligraphy improved – and he already had dozens of seal theories in mind that he couldn't wait to try out. Even now, he had a couple of seals on his wrists and ankles that restricted his movements slightly so that he could improve the strength of his limbs.

However, the redhead couldn't help but grow irritated every time he was praised by Jiraiya when he learned something that should've been taught to him a long time ago. It was embarrassing enough that he had three years on his graduating class and two on Team Gai due to failing the Academy three times and passing on what could only be best described as a "field promotion" after the whole Sacred Scroll Incident.

Sighing, he brushed a hand through his untamable red locks as he continued walking through the city streets and watching people use the waterways to travel faster. Altomare was a city that showed their pride in the ocean's beauty by having many "streets" within the city that were pure water while concrete streets bordered them. He could've easily water walked around the city, but Jiraiya had told him to keep a low profile since ninja were nothing more than myths and legends outside of the Elemental Nations.

Although, there was one thing that the outside world had that the Elemental Nations did not and had never seen before; creatures of varying shapes, sizes, and types that were practically everywhere. Even the fish of the outside world were merely more breeds of these strange creatures. Some of them were actually very interesting to look at while others seemed to be bland in their looks.

He chuckled as he saw a pair of ferret like creatures with brown fur run past him, squeaking happily as they scurried through the city. He couldn't deny that he was intrigued with these creatures and he wouldn't mind having one or two as companions, or possibly even friends.

He was brought out of everything as a ball of black gas and purple flames literally popped up right in his face with a face that showed nothing but playful mischief. He let out a cry of surprise and took an instinctive step back while the creature snickered at his expense. He sighed with a hand slapping and dragging his face in annoyance. This thing was _way_ too much like a ghost for his taste; which was an issue since he had a slight fear of them.

As it stopped snickering, it looked to the Uzumaki with a happy expression before it blew him a raspberry and faded away. "Geez," he muttered. "Didn't have to scare the crap out of me like that…"

_**"****You should've seen your face!"**_ roared a deep voice within his head as it laughed loudly at his expense.

_'Ah, shut up you damn overgrown floor rug!'_ retorted the man mentally to his tenant.

Let it be known that having a nine-tailed being of pure chakra and a subconscious sealed into you was not pleasant. No, most of the time Naruto and the Kyuubi were at each other's throats with threats and insults, but they were at least civil with one another on a certain level. It was a simple "scratch your back" relationship; Naruto gets strong enough to keep them both alive and Kyuubi supplies chakra every now and then when needed.

It wasn't much of a relationship, but at least it was something.

He resumed his walk through the city as a couple of those creatures raced past him in the canals, towing humans on boards at high speeds. He had heard that there was some race going on, but he didn't bother signing up. How could he without one of those creatures to help him anyway?

Sighing he passed by a small speedboat that had two women in it. One was blonde with twin tails that she had curled around both sides of her head while the other had a light blue hair color styled in hime way. They were both dressed in casual spaghetti strap shirts, pants that fell just above their ankles, and stylish sandals while shades covered their orange eyes.

As he passed, he faintly noticed that the one with blue hair was busy toying with some small electrical device he had never seen before while the blonde held a pocket size mirror and inspected her hair. When the blonde noticed him and their gazes met, she smirked and winked at him in a flirtatious way that made him look back to the street with the faintest of blushes on his face.

"Now that's interesting," commented the bluenette after the Uzumaki had gotten out of hearing distance.

"Oh? And just what is so interesting, Oakley?" asked the blonde.

The newly named bluenette smirked towards the direction Naruto was walking as she answered, "I was tinkering around with our scanner in case we found our targets, and it nearly shut down on me as he passed. The ratings he was giving nearly caused it to fry itself."

"That _is_ interesting," the blonde stated with a smirk of her own. "To think that hottie had a higher reading than our targets were theorized to have… I may just bag him after all." She licked her lips in a slightly provocative manner as she added, "Momma likes…"

"Get your mind out of the gutter, Annie," Oakley admonished with her smirk still in place. "Let's keep an eye out for the targets before we do anything rash. It could've just been a slight glitch after all. "

Pouting, Annie just crossed her arms and huffed out, "Fine." After that, Oakley started up the boat and they drove through the canals with their eyes peeled for their targets.

[With Naruto]

The redhead's brow was twitching a mile a minute as he felt the little ball of gas floating beside him again with that same grin on its face. Sighing while pinching the bridge of his nose, he stopped and looked to the gaseous being and asked, "What do you want? Isn't there someone else you can bother?"

To his dismay, the ball just closed its eyes and shook its head negatively without losing an inch of that damnable grin. It then surprised him by floating above his head and nestling itself right on top of his wild hair. It was interesting how something so gaseous looking could actually be solid as it pressed his hair down on his head.

Sighing in resignation, he decided to just let the little thing be and continue walking. So caught up in what had just happened, he never noticed he was going to bump someone until it happened and his arm knocked into a girl's shoulder. He stopped immediately and got a good look at her.

She had brown hair cut short with two horn-like extensions in the back, brown eyes, and a cute face. She wore a green top with a white collar, a short white skirt, forest green socks, and pink shoes with white bottoms. She looked to him warily, making him cringe and rub his head with a sheepish grin.

"Sorry about that, miss. I wasn't watching where I was going. I hope I didn't hurt you?"

She silently shook her head before giving him a small smile at his concern. It grew slightly as he sighed in relief.

"Thank Kami… I would've felt awful if you were. My name's Naruto; Naruto Uzumaki," he introduced as he held out a hand. She took it and shook it with her smile still in place before he asked, "Can I ask your name?"

She lost her smile at this and looked conflicted for a bit. It confused him slightly before she pointed a finger at her throat and opened her mouth without making a sound.

Eyes widening slightly, he asked, "You're mute?" At her nod, he gave her a reassuring grin. "That's alright. To tell you the truth, I probably would've forgotten it after we went our separate ways."

He rubbed his head sheepishly again while she made a giggling motion with her hand over her mouth in a cute manner. While no sound came out, it still looked adorable in his eyes.

They were brought out of their one-sided conversation by the small toot of a horn and they turned to see the two women from before on their boat as it calmly floated toward them. The redhead noticed that the bluenette had that same device from before in her hand and it was pointed at the both of them before it gave off a beeping sound. She then smirked as she took a glance at it, making Naruto tense and the creature on his head do so as well while the girl next to him looked frightened.

"Look here, Annie! We found one of our targets and that boy with the high readings!"

The blonde winked at the redhead and sultrily asked, "Hey handsome. Why don't you ditch the girl and hang out with a _woman_? I mean after all, she isn't even human."

His blue eyes narrowed and he stepped in front of the shaking girl while using an arm to put her further behind him. Taking a look over his shoulder, he declared, "Just stay behind me. I'll keep you safe."

While obviously scared and worried for him, she nodded and peeked out from behind him. The blonde pouted at the actions the Uzumaki made as she commented, "The world is so cruel to me… The only hottie in this city and he'd rather protect a Pokémon than spend time with me."

"Pokémon?" asked Naruto in pure confusion. "The hell is a Pokémon?"

The two women looked surprised at that question and Oakley asked, "You mean you really have no idea that the Gastly on your head is a Pokémon?"

"Uh… No? Should I know?"

The two looked at one another in pure confusion, giving Naruto the opportunity he needed to turn in place, scoop the girl in his arms, and bolt down the street with Gastly flying right after him. "H-Hey!" Annie called out in shock. "You can't just leave like that! You never even got my number!"

Oakley sweatdropped at her sister's antics as they both pulled out spheres with red tops and white bottoms; Pokéballs. Tossing them, the balls opened up and released a large orange and purple spider alongside a pink furred feline with a double tipped tail.

"Ariados, Espeon, go after them!" Oakley ordered, making them both give out sounds of acknowledgement and run after Naruto and the others.

With said Uzumaki, he was blazing down the streets as fast as he could without chakra so as to keep his low profile; though it was still odd to see an adult male running down the streets with a girl in his arms and a Pokémon flying after them. He was about to take a right turn before the girl suddenly pointed left, which made him immediately follow her direction. This went on for quite some time with her pointing the directions to take while he followed them without question.

They finally reached a small greenhouse with a dead end before he finally set her down. "Damn, no moving on," he cursed as he checked to see if they were followed. The girl stopped him when she grabbed his right arm and proceeded to drag him to the end of the greenhouse. When they stopped, she looked to him as he stared at the wall in confusion. "There's nothing here; just a dead end. We should try and find some other…place…to…"

He stopped short as he felt a shift in the air around the supposedly dead end of the area. Frowning, he reached an arm out to it and was surprised to see it go through without resistance as a blue light outlined the edges of his arm that was visible to him.

"An illusion," he muttered as he turned to the girl who was smiling at him and proceeded to walk right through the false wall.

Taking her lead, he stepped through with Gastly following before the three of them entered a beautiful garden filled with grass, some trees, a pond with a rock wall, and small streams of water pouring out of some holes in the wall. On one of the trees was a single swing that was made of two long ropes and a 2x4 piece of lumber.

"Wow," he gasped out at the sight before he smiled slightly. "It's beautiful…"

He felt a sudden increase of energy next to him and turned to the source, only to be surprised as the girl was engulfed in a bright light and _changed_ into a floating red and white creature. It had an aerodynamic body and glass-like down feathers. The lower half of its body was red with jet-plane wings, fin-like feet, and a blue triangular marking on its chest. Two white and red arms that looked like they could be tucked into its body were also visible. The upper half of its body was white with triangular ears and a red face that had a white pentagon in the middle. To finish it off, amber eyes filled with amusement and joy stared into his shocked azure orbs.

"Y-You're one of them; a Pokémon?" he asked in a soft tone due to his shock.

_"I am,"_ answered a female voice in his head that caused him to flinch since it was unexpected. The bird-like dragon cringed at his flinch as the voice continued, _"Sorry, I didn't mean to startle you, Naruto."_

He turned back to her and raised a brow in question. "Is that you talking in my head?"

The Pokémon nodded with a smile. _"Yes, and it's very nice to finally be able to talk back to you instead of having to stay silent. I never had any practice with talking in my human transformation since Bianca and Lorenzo are too busy to teach me. Also, to return the favor of you introducing yourself to me, my name is Latias. It's really nice to meet you, Naruto."_

"Latias," he repeated, testing the name on his tongue before he asked, "That the name of your species or is it _your_ name?"

She looked surprised at his question before she answered, _"It's the name for the female counterpart of mine and my brother's species, just as that Gastly is named the same as the others of his breed."_

"Oh, so it's a male," commented the Uzumaki, looking up at the floating ball, which nodded to confirm what Latias had stated. He then looked back to her and asked, "Haven't you ever thought about having a different name?"

_"No. I was born as a Latias and never really put much thought into my name. So, I never bothered to give myself one."_

"I see…" He then looked up to the Gastly and asked, "Well, do _you_ want a name, little guy?" The Pokémon grinned at him and began to float around his head in circles as it chanted its breed's name over and over, much to Naruto's confusion.

Latias giggled at his confusion and informed, _"Most Pokémon who aren't able to perform telepathic or human speech are left with just the name of their breed as their way of communication. However, it naturally is translated between Pokémon for a sense of understanding. Gastly's happy that you'd offer him a name. He seems to have taken a liking to you, Naruto."_

"Geez, the more I learn about you Pokémon, the more questions I end up getting. Hmm, let's see now… How about…Yurei?" offered the redhead, making the ghost Pokémon stop flying around and give a thoughtful expression. After some time, it grinned and nodded happily before it did the unthinkable…and gave the whiskered man a big slobbery lick to his face. Grimacing at the saliva, he offhandedly stated, "Okay then, Yurei it is…"

_"It's a nice name for him,"_ commented Latias with a smile. _"I'm almost tempted to see what you would name me. Anyway, back to the point of me bringing you here… This place is a sanctuary for me and my older brother, Latios. It was offered to us so that we had a place to come to if we ever needed one while we watched over the city."_

"What do you mean?"

_"What I mean is-"_

"Hey, what the heck is going on?!" yelled a female voice, making the three of them turn to see a girl who looked _exactly_ like the disguise Latias took in the city, with the addition of a white hat on her head. She was glaring at the redhead as she marched over and got in his space, poking his chest accusingly. "Just what do you think you're doing here?! This place is meant to be a secret from the public with only myself and my grandfather knowing about it!"

Looking worried, Latias floated between the two and stayed in front of Naruto, much to the girl's surprise. _"Bianca, it's okay! I brought him here after he saved me from two women who looked way too interested in us. One of them even called me a 'target' and they both saw through my disguise. Naruto here saved me when he saw an opening by taking me away and I directed him here."_

Bianca was both shocked and worried at the news. Some women were after her friend for some reason and this guy was fortunate enough to be in the area and take her to safety. Turning to the whiskered man, she bowed slightly and apologized, "I'm sorry for jumping the gun on you. I thought you snuck in here and were trying to get to Latias. I'm Bianca, an aspiring artist and resident of Altomare."

She held out her hand and he was quick to shake it with a smile. "Nice to meet you, and don't sweat it. It's not the first time I was accused of something without question. I'm Naruto Uzumaki, a traveler from across the ocean. I came here with my teacher, Jiraiya, before he practically ditched me for who knows what reason." He then pointed to the ghost Pokémon and added, "This is a Gastly that followed me ever since I was on my own in this city. I call him Yurei."

Nodding, Bianca turned to Latias and asked, "Does your brother know?"

The Pokémon did something that made Naruto want to burst out into laughter; she rubbed the back of her head with her claw and had the same sheepish look he had given her earlier. _"Well, I didn't exactly get the chance to…"_

_"Then why don't you do so now, sister?"_ suggested a male voice, making them all turn to see a larger and blue colored version of Latias floating down from the canopy of tree tops that blocked most of the sunlight. His eyes were red in color and the triangle on his chest was of the same coloration, but he just looked like a male and blue colored version of Latias to Naruto.

_"Brother!"_ greeted Latias happily as she floated over and hugged the larger Pokémon. Gesturing to Naruto, she began, _"This is-"_

_"I know what this man's name is and what he did for you. I heard it from when you stopped Bianca earlier."_ Turning to Naruto, Latios floated over and looked directly into his blue eyes with their faces about a foot apart. _"I'm curious as to why a human would go out of his way to help my sister other than personal gain… Most humans only look out for themselves, after all."_

Standing his ground, Naruto replied, "Maybe humans are that way, but I know for a fact that I wouldn't help someone just for my own benefit. I've never had much in life, and I never needed much to survive. Besides, I've never even heard of you Pokémon before I came to this city since my part of the world doesn't have a single one to my knowledge."

Latios narrowed his eyes at Naruto, making both Bianca and Latias nervous about what he would do. _"You do seem different from others… However, I won't trust you on words alone." _Poking his chest gently yet firmly with a claw, the Pokémon finished, _"I want to see just what kind of person you are, and to do that I will view your memories. Your mind can never lie unless it has been tampered with, and if yours is then I will fix it before seeing your memories."_

"Deal," agreed the redhead as Latios placed a claw on his forehead and the two closed their eyes. Emptying his thoughts so Latios could get better access, Naruto made no form of resistance as the Pokémon saw every moment he had ever experienced in life…starting with his childhood.

_"Monster!"_

_"Demon!"_

_"Why don't you just run off and die?! No one wants you!"_

_"You fail, Naruto!"_

_"You've failed again, Naruto!"_

_"I'm sorry Naruto, but you've failed once again…"_

_"YOU are the nine tailed fox! And now, you'll DIE!"_

_"My first impression of you guys is…I hate you."_

_"Naruto-baka!"_

_"Dobe…"_

_"Brats who bark loudest are usually the weakest…"_

_"Shinobi who break rules are scum, but those who betray and abandon their comrades are even worse than that…"_

_"You aren't hurt are ya, scaredy cat?"_

_"I believe we are truly strong when we have precious people to protect…"_

_"**Five Prong Seal**!"_

_"You'll be Hokage?! Ha! Not a chance! Tell ya what; I'LL be Hokage for you!"_

_"No one can defy fate! You have no idea what it's like to have a brand that will NEVER go away!"_

_"There's no way… NO WAY THAT I'LL LOSE TO A GUY LIKE HIM!"_

_"Still the same child spouting his head off about becoming Hokage, eh Naruto-kun?"_

_"Please…bring Sasuke-kun back to me!"_

_"So it's you…hopeless little knucklehead…"_

_"**Chidori/Rasengan**!"_

_"If being a fool means what you say, then I'll remain a fool my entire life!"_

After the flashes of memories were over, the blue dragon floated back slightly and looked to the Uzumaki who had his gaze rooted to the ground. It stunned him that this human could have such a life with far more negative memories than positive, let alone having something as ominous as the Kyuubi sealed into his body. Looking to his sister, he nodded once and spoke.

_"Well…you've certainly had your fair share of hardships… I suppose you're trustworthy after all. However, I still need you to leave so that I can discuss what I've seen with Bianca and my sister. I'd like to do it without your presence so that they can think over what will be told before you return. Is this acceptable?"_

Naruto wordlessly nodded and headed for the exit with Yurei in tow before he was halted by Latias' voice. _"Be sure to come back, Naruto. Even if I learn about you, I want to hear it from you later."_

He turned back and saw her smiling at him reassuringly, which made his give a small one in return. "I will…"

He then left the garden and made his way back to the streets of the city while leaving a small seal tag on one of the bricks of the greenhouse. It was a simple marker so that he wouldn't get lost on the return trip.

Once again stepping onto the streets, he made his way to the main plaza of Altomare in hopes of finding some food for himself and his companion. It was a peaceful trip and he couldn't help his smile when he saw and felt the content atmosphere in the air from the citizens. If he had visited this place as a young boy many years ago, he would've easily decided to stay and start a life here.

He was brought out of his thoughts at the sound of a young boy exclaiming in awe at the many sights of the city. Turning, he saw three humans along with two of those Pokémon hanging around with them.

The first was a young boy, not even in his preteens, that wore black shoes, light blue jeans, a black shirt with a blue and white short sleeved jacket, and a red and white hat with a green symbol on it. He had black hair, reddish brown eyes, and the thing that stood out the most about him was the birthmarks on his cheeks that looked like small lightning bolts. His hands were covered in green fingerless gloves and he currently had five Pokéballs clipped to his belt while a yellow mouse like Pokémon rested on his shoulder.

Next to him was a teenage girl with short orange hair that had a single tail on the side and green eyes. She wore a short yellow shirt that stopped above her stomach, blue shorts that reached halfway down her thighs with red straps going from the beltline to her shoulders, red and white sneakers, and a red pack on her back. In her arms was an egg-like Pokémon with a spiky head and a cheerful expression.

The last member of their group was a man with dark skin, spiked dark brown hair, and squinted eyes. He wore a green vest over an orange shirt, maroon pants, and dark blue shoes while giving off an air of slight wisdom.

"Ash, relax!" chastised the girl to the boy named Ash. "People will think you're off your rocker with how loud you're being."

"I can't help it, Misty! This place is just so nice and that race we were in was awesome! I just wish Totodile and I would've won."

The older male chuckled as he held out a small booklet and looked through it. "That race is held every week, so it's one of this city's main attractions. The real clincher for tourists is the legend of the two guardians and the Soul Dew."

Curious about the supposed legend surrounding Latias and her brother, Naruto decided to make his presence known. "Excuse me, but I'm curious about that legend you just mentioned."

The dark skinned male turned to the redhead and smiled as he held out the booklet. "Here, this should tell you about it. My name's Brock and these are my friends Ash and Misty."

"Nice to meet you," the orangette greeted with a smile before she looked to her Pokémon. "This is Togepi. Say 'Hi' Togepi!" The little guy just chirped happily at the Uzumaki.

"I know you were just told, but my name's Ash from Pallet Town, and this is my buddy Pikachu!" The mouse waved and exclaimed its name happily in greeting.

"Naruto Uzumaki and I'm from the Elemental Nations across the ocean. The Gastly is a Pokémon that decided to follow me, so I named him Yurei." He then skimmed through the booklet and read that the legend spoke of a parent Latios that guarded the city before its soul became the Soul Dew, leaving the city in the care of the two dragons he had just talked to. "Interesting… I've always like legends since they always have some cool story to tell."

As Naruto handed him the booklet back, Brock asked, "So, if you don't mind me asking, why are you here in Altomare?"

Shrugging, Naruto answered, "I'm on a trip with my teacher away from home for three years. This is supposed to be our last stop before we head back home in a couple of days. What about you guys?"

"We came for the races and to see what kinds of Pokémon are here," Misty answered. "Speaking of which, why haven't you captured that Gastly? I would've thought you'd do so if it likes you that much."

"Capture? What are you talking about?"

Blinking in surprise, the three of them looked to Naruto as if he had two heads. "Well, usually trainers capture Pokémon in Pokéballs; like these," Ash answered while holding up two spare Pokéballs from his back pouch. "Once captured, they're your Pokémon and they can be used for anything such as a battle, as a friend, or even both. Here, take these."

Naruto hesitantly took the two spheres and pressed the button on one of them, making it double in size. "Strange… I've never seen anything like this before."

The others watched him inspect the Pokéball before suddenly Yurei took matters into his own metaphorical hands and floated down to the activated ball. Pressing the button, the ball opened up and sucked him inside in a red flash of light that shocked Naruto before the ball dinged.

"There, now that Gastly is your Pokémon," Brock informed him. "You can let him out by pressing the button, tossing the ball, or vocally commanding it."

Humming in thought, Naruto simply pressed the button again and let Yurei back out into the open before he took his place in Naruto's hair. "Welcome back, buddy."

_**"Interesting… So the humans on this side of the world don't use chakra, but rather these Pokémon that they 'capture' to complete tasks. At least you have one now and have an extra ball to capture another."**_

_'I guess… But I wonder which one I'll find that wants to come with me.'_

Pocketing the Pokéballs, Naruto nodded in thanks to the three of them before scratching his cheek with a sheepish grin. "Thanks, but uh…I don't have anything to return the favor."

Ash, being a trainer who loves a good match, suggested, "Why don't we have a Pokémon Battle before you leave? You can look for another one here in the city so that we can have a two-on-two fight."

Thinking it over, the redhead shrugged and shook the boy's hand. "Deal; I'll have a battle with you before I leave. Now, if I'm gonna have one with you, I guess I should look for another partner…and find out how exactly I _do_ a Pokémon Battle."

The three looked surprised again, though not as much as before, at his words; but they were unable to say anything as he bid them goodbye and walked off. As he left, Misty turned to Ash and pinched his ear scoldingly. "You dumbass! He didn't know about capturing Pokémon, so what makes you think he knew how to _battle_?!"

"B-But Misty-!" Ash tried to explain, but she was having none of it as she dragged him off after Naruto with Brock in tow so that they could find and explain how battles work to him.

Meanwhile, Naruto was strolling once again through the city in hopes of finding a new partner. He decided to try some of the back alleyways in hopes of finding one hanging around there, but he had no luck so far. He rubbed his head with a sigh as he walked through his fourth alley and came up empty-handed.

"Never thought it'd be this hard when I'm _actually_ looking for a partner (2)," he commented. Deciding to take a break, he sat on a nearby bench and rested his arms on his knees with his body hunched forward. "I wonder if I'll be able to find one in time," he mused before shifting his foot and accidentally kicking a can. The noise caused a cry of surprise to erupt from beneath the bench and he looked under his seat to see a wary looking Pokémon shaking in slight fear.

It was a small, green reptilian Pokémon with rocky skin. It had a blunt spike on top of its head, a short rounded snout, and triangular black markings below and on the upper corners of its red eyes. Red scales covered its diamond-shaped belly, and there were several small holes in its body. Its short arms lacked fingers, while its feet had a single toenail each. It had a tail with a conical center surrounded by a ring of plate-like scales, causing it to resemble a tunnel-boring machine of some sort.

Grinning in hopes of calming it down, Naruto softly said, "Hey, little guy. Don't worry; I'm not going to be any trouble." Seeing it still look wary, he decided to appease it and take a couple of steps back from the bench. With the space widening, the Pokémon calmed slightly and slowly crawled out from under the bench, making Naruto smile. "There you go! Why don't we introduce ourselves? I'm Naruto and this is my friend, Yurei."

The green Pokémon looked to the Gastly, which grinned at her in a friendly manner. Turning back to the whiskered human crouching some feet in front of her, she stated her name, as was the norm with Pokémon species. "Larvitar…"

Grinning, the redhead slowly pulled out his unused Pokéball and set it down in front of him without making any sudden movements. With his arms rested on his crouched legs, he stated, "You know, you look like you could use a friend in this city. It already looks like you're not all that fond of this place, considering how you keep eying the water canals."

True to his word, the Larvitar kept giving side glances to the canals with a nervous look. It was understandable given her rock and ground affinities; both of which were incredibly weak to water. She turned back to him and gave him a nod for him to continue.

"I'd be happy to be your friend and get you out of this city. Problem is, I won't leave for a couple days and to get you out, I'd need to have you become my partner." Motioning the resting Pokéball, he continued, "You look like you know how to take care of yourself, but I'd still like for you to come with me. I'll show you places that I bet you've never seen before, and I can help you get stronger too." She snorted at him in amusement, challenging his claim. "Don't believe me, eh? Alright then; look at this."

Holding out his hand, he let a sphere of chakra form and it began to spin rapidly while covering his form and the two Pokémon in a light blue hue. Larvitar gaped in shock at the **Rasengan** in the redhead's hand and she took a step closer before it dissipated.

"Sorry, but I wouldn't do that. The **Rasengan** is not something to take lightly since it can grind through metal when I put effort into it." He kept his smile to her and gently tapped the Pokéball as he asked, "So, do you want to become my new partner? I promise that I will never abandon you or hurt you in any purposeful way, and I never break my promises since it's my ninja way."

She looked into his eyes, her red ones narrowing slightly as she searched for any deceit. When she found none, she stepped up to the ball and looked up at him again with a nervous gaze. He smiled warmly and gently rubbed her head, making her ease up enough to smile at him. Making her decision, she poked the button and allowed herself to be taken by the red light. The ball shook just once before dinging again, making Naruto pick it up with a smile.

"Welcome to the team," he said to the sphere before he let her out again. When she saw him, she smiled and cried out her name happily. "Alright, now all you need is a name. It gives you a personality and makes you unique among others." She nodded and waited for him to decide while he cupped his chin in thought. "How about…Gojira?" he offered. She made a thinking face before nodding once with a smirk and crossed arms, which made the Uzumaki chuckle. "Alright then; Gojira it is!"

"How nice for you," commented a familiar voice that made Naruto freeze. He turned and was surprised to see Annie and Oakley on their boat with their Pokémon on the bow. It was Oakley who had spoken and she continued with, "Too bad you won't be able to keep your promise to her!"

She held up a strange looking weapon and fired it, shooting a dart into Naruto's arm that made him cringe before his head started swimming.

"Larvitar/Gastly!" cried out his Pokémon in concern as he fell to a knee.

His vision blurred as he whispered to Yurei, "Take Gojira and find Latias and Latios… Tell them…what…happened…"

With that, he fell unconscious and Yurei quickly grabbed Gojira with his tongue and flew off, leaving the two women with their prize. Gojira made to reach out to their quickly distancing forms as she cried her name for Naruto. Yurei took a glance back as he kept flying before he forced himself to go faster to find the others. He wouldn't lose his new trainer and neither would Gojira.

He swore he'd find the others and rescue Naruto before something awful happened.

**(End Chapter)**

1~ Think of Naruto with N's hairstyle, but red

2~ You ever notice how _true _that statement is?! I can never find the Pokémon I'm searching for unless I'm doing something else in the games!

So, what did you guys think of the first chapter? I hope it turned out well and made you eager for more!

Note: Naruto won't be getting anymore Pokémon on his team, but he will meet others on his journey! Plus, _two_ of them will take an active interest in him! *winks*

Now, I'm sure you guys have plenty of questions or concerns. If you do and would like them answered, please PM them to me and I will get back to you as soon as possible! Also, be sure to review this story! Please and thank you!

Next Time: Naruto captured and a city taken! Will he and Altomare be saved?! Stay Tuned!

**pain17ification**


	2. Chapter 2: Saving Graces

Hello FanFiction! This is pain17ification with the next issue of "Evolving Bonds"! I hope you all enjoy the chapter!

Please Note: Due to difficulty trying to make PokéMoves typed in Japanese, all techniques (both chakra and PP based) will be portrayed in English!

Second Note: I have decided to keep this a single pairing only with Naruto and Latias! However, Mew will still have a big role and will still bond with Naruto!

Disclaimer (aka: pain in the ass): pain17ification doesn't own anything except for the story idea

"Speech"

'_Thoughts'_

**Techniques**

_**Bijuu**_

_Radio/TV_

"_Telepathic"_

[Scene Shift]

**Chapter 2: Saving Graces**

_**"****So…exactly how long are you gonna play dead, brat?"**_

_'Just long enough for them to take me to wherever they have their base of operations. Thanks for the quick system purge by the way, fox.'_

_**"Bah, something as simple as a knockout serum is child's play to me. Still, it did have a different composition than ones I've purged before."**_

_'Not surprising since we're so far away from home. Hey fox, does the energy these Pokémon have feel similar to chakra?'_

_**"Somewhat; however it isn't enough to fully copy without a catalyst to let it adapt to your system. Why do you ask?"**_

_'Just curious is all… I mean, now that Yurei and Gojira are my Pokémon, it'd be cool if we could use some similar moves in battle. It'd really give me an edge on the Akatsuki…and Sasuke.'_

The Kyuubi fell silent at that, thinking over the potential of the idea before an idea began to grow in its head. It was a stretch really, but if it worked then Naruto would only benefit from it and have a better chance at staying alive.

The boat came to a stop and Naruto felt himself get lifted in the air by a strange energy. His floating body was taken inside of a large observatory styled building before he was placed inside of a barred cage.

"Espeon, keep an eye on him," ordered Oakley. "If he wakes up, knock him out with your **Hypnosis**."

The Pokémon nodded and sat in front of the cage much like a feline would while the women left to tinker with a strange device. _**"Looks like you're stuck playing captive, brat."**_

_'Tell me something I don't know…'_

**"**_**You're mother was my second container while Mito Uzumaki was my first."**_

_'WHAT?!'_

**"**_**You wanted to hear something you didn't know; so there,"**_ cheekily replied the Bijuu.

_'I never expected you to actually _indulge_ me, you damn furball!'_

He had to seriously keep himself from twitching his brow as the fox roared with laughter in his mind.

[With Yurei and Gojira]

The two Pokémon quickly moved through the streets of Altomare in search of Latias, Bianca, or Latios. Yurei was taking the lead since he was familiar with Latias' energy signature while he held Gojira in his long tongue.

The little Larvitar was worried sick for Naruto. She didn't want to go search for anyone when she could've tried to help him. He was kind to her, and she felt as if she could trust him with her future. It shook her to the core when she lost her potential trainer just moments after she accepted him and he named her. However, Yurei took charge of the situation and she'd follow his lead; as if she had a choice given her current position.

Yurei had just turned another corner before he ran smack into a familiar Pikachu. The collision made him release Gojira who huffed in annoyance at being dropped so carelessly. "Pikachu, are you alright?!" asked a voice familiar to the ghost Pokémon.

"Gastly!" he cried out, getting the attention of Ash and his friends.

"Yurei?" asked Misty in surprise. "What are you doing here? Where's Naruto?"

Gojira, growing annoyed and worried, began crying out angrily and gesturing wildly in hopes of quickly giving them the message. However, the trainers were unable to understand them while Pikachu was surprised at what she was saying. As soon as she finished her ranting, she stepped up to Yurei and, with a firm grip on his tongue, began to drag him down where they were originally going.

While the humans sweatdropped at the Larvitar's actions, Pikachu started to tug on Ash's pant leg in urgency. "You want to help them? But we don't even know what they want from us."

Pikachu just tugged once more before he followed after them, taking Notice of Gojira once again taking lead with Gojira secure in his tongue again. The boy narrowed his eyes in confusion before he took off after his friend with Brock and Misty following behind him.

[Hidden Garden]

Latios had just finished telling Bianca and his younger sister about what he had seen during the mind link he performed with Naruto. He helped get the point across by using his psychic power to create projections of some of the memories against the water, almost like a television.

_"I've never seen such...sadness in a single life. From his first memories, he's lived in fear and despair while holding onto a small shred of hope,"_ stated the blue dragon.

"That's horrible," whispered Bianca, having to sit down from the shock. "How could he have lived like that without snapping at some point?"

Latias was silent as she had a look of pure sadness on her face. Naruto was nothing but kind to her and he had protected her from those female Pokémon hunters. To see his life as..._that,_ was nothing short of surprising.

_"I have no doubts about his intentions after what I've seen,"_ continued Latios. _"Based on his reaction earlier, he's more than like afraid of us rejecting him due to his...condition."_ He turned to his sister and saw that she was lost in her thoughts. _"Sister."_

_"Huh?"_ she asked in surprise at being broken from her musing.

_"He seems to trust you, considering what he did for you and how quick he was to listen to your directions in getting here."_

_"Yea… I suppose,"_ she answered, unsure of where he was going with his words.

_"Perhaps if you were to reassure him that we do not see him as the beast he carries, then he could potentially become a very powerful ally. You do know of the current unrest among the higher Pokémon, right?"_

She narrowed her eyes at that and nodded. _"I never thought things would escalate so badly after a few altercations with the humans. Is Arceus really needed in this issue?"_

"_I'm not sure, but just the _mention_ of his presence is cause for worry."_

"What are you two talking about?" queried an extremely confused Bianca.

_"An issue between humans and Pokémon. It's nothing for you to worry about,"_ reassured the blue dragon before his eyes flashed and he turned to the garden entrance in time to see three Pokémon leading three humans inside. _"What is the meaning of this?"_

_"Yurei?"_ asked Latias as the ghost Pokémon quickly flew into her face and began frantically telling her what had happened, making her eyes widen in panic. _"Naruto was taken by those two from before!"_

"What?" asked Bianca in shock. "But how did they-?"

She was cut off when a large machine broke through the rock wall of the garden followed by a mechanical arm reaching out and snagging Latios in a firm grip.

"Latios/_Brother_!" cried out Bianca and Latias in surprise.

The top hatch of the machine opened up to reveal Annie and Oakley, who both had matching smirks on their faces. "Thanks for leading us right to the prize, you little ghost," declared Oakley as a second, but smaller, arm reached right into the water and pulled out a glowing gem. "The Soul Dew is ours!"

"See ya around!" stated Annie as the machine took off with Latios in tow.

Quickly taking charge, Bianca led the others outside and they hurried off to her home where a boat was waiting. Latias carried Gojira since she was the slowest and she could see the worry on the little Pokémon's face. She herself was worried as well, for both her brother and for Naruto.

_'Please, both of you be okay.'_

[Altomare Museum]

Naruto sighed in annoyance as he gently placed the unconscious Espeon to the side of the spacious room he was in. It was relatively easy to knock out the Pokémon with a quick burst of Kyuubi's chakra, which scared it into its current state.

Naruto silently walked around with his gaze taking in every detail of the museum and his ears focused on anything that would make a sound. He stepped up to the strange device that the two women were tinkering with and narrowed his eyes at it.

_'So, this is the Defense Mechanism of Altomare (DMA)... It's...impressively big.'_

_**"****You don't honestly expect for a town of this size to have anything less for protection, right?"**_

_'I suppose not… But they said that they needed the Soul Dew to power it up. That means that they'll go after Latias and Latios.'_

_**"****Not 'will' go after, brat; 'have gone' after. I can feel the elder Pokémon's signature coming along with those two women. Stay hidden and wait for the right moment."**_

_'Right...''_ agreed the redhead before he leapt high up into the air and clung to the ceiling with his chakra, idly noting that a large skeleton of a dangerous looking creature hanging next to him and another was displayed below him.

Not even a minute after he got out of sight, Annie and Oakley walked in with Latios in a strange net-like prison that shocked him whenever he moved, making Naruto suppress an enraged growl. He then saw Oakley pull out a glowing gem which was no doubt the Soul Dew. Meanwhile, their Ariados pulled Latios into the center of a strange pedestal and he felt a small chill of worry go down his spine.

His eyes widened in shock as the three ringed outer layers of the pedestal began to rise along with Latios before they started to circle him in a locking manner. Meanwhile, the pedestal began to glow with a bluish green light that traveled across the line-like designs on the ground. Suddenly, the cage surrounding the device opened up and sank into the floor, revealing the DMA.

"Perfect," Oakley stated with glee. "Just like the book said."

"Now what?" Annie asked.

"Now, we only have one more thing to do." Oakley then carried the Soul Dew over to the device and prepared to place it in.

Meanwhile, Naruto quietly dropped to the ground and snuck around so that he could get close to Latios. When he was within decent range, he called out in a hushed tone, "Latios, open your eyes!"

The blue dragon stirred in his prison and weakly cracked his eyes open before he felt a familiar presence next to him. Turning, he saw that it was Naruto, much to his surprise. _"What are you doing here?"_

"Saving you; now brace yourself," ordered the redhead as he went through a few handseals before he called out, "**Replacement Jutsu**!"

In twin plumes of smoke, Naruto and Latios had switched places, much to the Pokémon's shock. Naruto gave him a firm nod before the women noticed what had happened.

"What the hell?!" Annie called out in surprise while Oakley glared angrily before suddenly gaining a menacing smirk.

"Fine then… You want to take his place, I'll let you!" she declared before she placed the Soul Dew in the DMA, which caused the bluish green light to change to a vicious violet while Naruto grit his teeth to keep from crying out in pain. The device was shocking him with hundreds of volts of power while his own, along with Kyuubi's, was being siphoned. Meanwhile, the DMA was activating and lowered the control seat for Oakley to get in.

Through the pain, he grit out, "Latios, get out of here! Find the others!"

The blue dragon nodded and shot off at high speed, making Annie call out in worry, "It's getting away!"

"Not for long," called Oakley from the control seat, using the panel to guide the siphoning energy into restoring the two skeletons Naruto had seen earlier.

When they were fully restored, two dangerous looking Pokémon appeared. The first was a large, bipedal Pokémon with a large head that had two vicious eyes, pointed ears and a mouth full of serrated fangs. It had light violet-gray skin over much of its body with two pale violet membranes stretched between its arms and sides. It also had plate-like spines going down its back, leading to its strong, triangular spade-tipped tail while its talon-like feet looked easily capable of scooping up and tightly clutching its prey.

The second had a body closely resembling a living skeleton with a half-moon, disc shaped head that had two small, forward facing eyes. Its body had a light gray chest plate with a brown shell resembling a visible backbone, containing three ribs protruding on each side and a thick pointed tail. It didn't have hands, but instead had large, sharp, gray scythes while its legs are brown and thin, leading into small feet with two large gray claws.

"Aerodactyl, Kabutops, bring back Latios and get Latias while you're at it!" ordered Oakley as the two revived Pokémon took off. Turning back to the controls, she began to use the power of the DMA to block off the city streets so that the others would have a much harder time interfering.

Naruto growled as the pain intensified and more power was taken from him. _'Kyuubi, can't you do something?!'_

_**"****You're the dumbass who decided to take that Pokémon's place, fool! That machine is affecting me as well; how the hell do you think **_**I**_** feel at the moment?!"**_

_'Can't we just overload it?!'_

_**"****Not wise since we're still connected to it!"**_ it called back through the growing pain. _**"We'd both be killed while our combined chakra would explode outward and destroy a large part of this city!"**_

_'Dammit!'_

[With the others]

Quickly taking her grandfather Lorenzo's boat, Bianca and the others hurried to the museum in order to save Latios and Naruto. Latias and a few of Ash's friends' Pokémon helped speed things along by pulling on the boat with ropes.

Suddenly, a loud screeching roar filled the air and Yurei called out in surprised as he noticed Aerodactyl coming in for a dive bombing strike. He turned to Gojira and Pikachu and they both nodded before they all readied to counter strike.

The others noticed as well and they braced themselves for the revived Pokémon's attack. "Pikachu, use a **Thunderbolt**!" called out Ash and the mouse-like Pokémon complied with a charged up shot of electricity. Yurei gathered an orb of violet-black energy before he unleashed his **Shadow Ball** attack while Gojira picked up sand and dust for a **Sandstorm**.

Aerodactyl barrel rolled away from the **Thunderbolt** before it swatted away the **Shadow Ball** with its wing and rode through the **Sandstorm** without an issue.

"Not good! It's too strong!" Brock cried out in worry as the Pokémon got closer.

"What do we do?!" Bianca called out as Latias, Noctowl, and Crobat kept pulled the boat as fast as they could. "It's gaining on us!"

Latias turned back to see the Pokémon before she felt a small essence of Naruto's energy within it, making her growl in anger at what he was forced to do. Shaking off the rope she was pulling, she turned and flew like a bullet at Aerodactyl before she rammed into it and tackled it into the water.

"Latias!" called the others before Pikachu noticed Kabutops blazing down the streets with its slim frame.

"Pika...CHU!" it cried out while releasing shot after shot of **Thunderbolts** in hopes of hitting it. However, it was too quick and swerved out of the way of each shot before it tensed its legs and leapt at the boat with its blades poised to strike.

"Look out!" Misty cried before a stream of light shot out and struck Kabutops, knocking it back.

"Latios!" called Bianca in surprise before she saw him charge up an **Ice Beam** and fire it at Kabutops. The arcing beam of frigid power struck true and froze the revived Pokémon to a wall where it struggled to get free.

After making sure Kabutops wouldn't get out soon, he turned to Bianca and ordered, _"Hurry to the museum! Naruto is being used to power it up!"_

She nodded and revved up the boat so that it continued toward the museum while Latios and Latias held off Aerodactyl. It roared furiously at them and charged up a **Hyper Beam** before it fired, forcing the two eon dragons to evade and take to the maze-like canals in hopes of losing it.

Aerodactyl chose to go after Latias and dove towards her as she kept a fair distance with her sharp turns and knowledge of the city streets. Mentally reaching her brother, she called out, _"I'm going to lead it to the museum!"_

_"Are you sure you can make it there without help?"_

_"Yes, I'll be fine! Now go! I'll meet you and the others there!"_ she reassured him as she cut off the link and increased her speed to the museum.

Back with Ash and the others, they had just reached the museum after barely escaping the sudden rising water formed from the DMA. They rushed inside just in time to see Annie standing next to the machine while Oakley sat in the controls and Naruto was struggling to stay conscious.

"Naruto!" called Bianca in concern as she and the others rushed over to help him. However, they were cut off by Ariados leaping into their path along with an awakened Espeon.

"So sorry, but this battery still has plenty of juice left in him!" declared Oakley as she grinned with a power drunk expression on her face. "Annie, take care of them while I finish taking control of the city!"

The blonde smirked and stepped up behind their Pokémon and in front of Naruto's prison. "Let's see what you got!"

"Yurei! Gojira!" called Naruto in an obvious struggle to speak. "Help Bianca and the others handle them! I'll get out somehow!"

Gojira looked to him worryingly before Yurei gave her a reassuring nod. She nodded back and gave the two Pokémon a fierce glare before she reared her head back with a small flame growing in her mouth. With a roar, she shot it forward and unleashed a torrent of fire known as **Flamethrower** at Ariados. Meanwhile, Yurei flew around the room and fired a barrage of **Shadow Balls** at Espeon who leapt out of the way and retaliated with **Psybeams**.

Ariados barely avoided the fire attack but it didn't count for Pikachu suddenly coming up with a **Quick Attack** that knocked it to the side in time for Gojira to fire a **Sandstorm** at it.

Unable to avoid this one, the spider-like Pokémon was blasted back into the wall and knocked unconscious. Back with Yurei, he was finally hit by one of Espeon's **Psybeams** and knocked back into one of the museum pieces.

"Yurei!" Naruto called out in concern before he grunted and convulsed slightly in pain. With one eye clenched shut and the other cracked open, he watched his first Pokémon and friend struggle to float back up. "You can do this, Yurei! I know you can!"

The Gastly looked to his trainer in pain before his form began to glow a bright white, much to everyone's surprise. When the light died down, a new Pokémon stood in Yurei's place.

"I-It evolved!" gasped Misty in whispered awe since seeing evolution was always a spectacle.

In the place of what was once a Gastly was a purple Pokémon with a gaseous body. It had a round head along with a pair of floating disembodied hands while each hand had three pointed fingers. Its head was flanked by three large, spiked protrusions on either side, and its eyes were large and triangular with small pupils. The gases composing its head curved down to form several pointed teeth framing a pink mouth and a long tongue while its body tapered into a jagged tail.

"Haunter!" cried the new Pokémon before it faded from view and quickly reappeared in front of Espeon before punching it square in the face with a shadowy hand.

"That was **Shadow Punch**!" Bianca exclaimed in surprise as the Espeon struggle to get up before it was hit directly with a **Shadow Ball** and knocked into the wall next to Ariados.

"No!" Annie called out in concern as she ran over to the downed Pokémon. Seeing that they weren't getting up soon, she quickly returned them to their Pokéballs and called out to Oakley. "We're out of Pokémon!"

"Oh no we're not!" replied the bluenette as she turned her control seat to the entrance just in time to see the eon dragons rush in followed by Aerodactyl breaking right through the entrance. It roared at them while they growled in response.

Latias then noticed Naruto convulsing in pain and she quickly flew over to help him, only to get repelled by the energy field surrounding him. _"Naruto! Hold on, we'll get you out!"_

He struggled to look at her before his eyes widened in shock, making her turn to see Aerodactyl coming in for a rushing attack. It got closer and closer before it was pushed back by the combined efforts of Latios' **Luster Purge** and Pikachu's **Thunderbolt**. The blue dragon then flew over to them and began to bash against the energy field.

_"Hang on, Naruto!"_ he called out as he kept bashing it followed by Latias. Yurei helped out with continuous **Shadow Punches** while Gojira kept up a steady stream of her **Sandstorm**.

"Tch," scoffed Oakley before she pulled out a small gun and fired an electrical net trap that caught Latias, making her cry out in pain and fall to the floor.

_"Sister!"_ cried Latios. He went to help her but was knocked aside by Aerodactyl's large tail.

Naruto looked on in horror as Latias convulsed continuously in pain and his normal blue eyes turned a furious crimson with a black slit pupil. Inside the seal and through the pain, Kyuubi looked on in surprise as new pipes began to form on the ceiling next to the blue chakra one and red chakra one. One of them looked like a purplish orange flame while the other looked to be a pure black aura. _**"How did he-?"**_ it began before it realized exactly how the new pipes came into existence.

The conflicting energies of chakra and Pokémon power (poképower) along with the stress on both Naruto and the seal caused his chakra coils to take in any energy it could to keep him alive. The result was Naruto gaining two types of poképower, though the fox didn't know which types at the moment. However, it soon identified one of the types when Naruto suddenly acted.

With a roar, Naruto unleashed a wave of oppressive dark power that opened up the energy field enough for him to squeeze out and land on all fours. His breathing was ragged, his body hurt like hell all over, and he still saw Latias crying out in pain.

He slowly stood up with his head down, making the others look to him in worry while the machine started sparking due to the loss of a power source. Aerodactyl however merely saw new prey and charged with a roar. Naruto in response snapped his head up, showing everyone his eyes that were pools of black, and he struck with a clawed hand that was covered in dark power.

"**Night Slash**," he stated in a deathly calm tone before he blurred right past Aerodactyl with his right claw outstretched. The revived Pokémon suddenly cried out in pain as several large gashes appeared on its body. In rage, it turned back around and covered its form in a yellowish purple glow before it charged at Naruto.

Naruto leapt high into the air and charged a **Rasengan** in his hand that soon had dark power mixed into it. It began to rage in an unstable manner as he plummeted down to meet Aerodactyl's charge.

With twin roars, the fossil Pokémon's **Giga Impact** met Naruto's **Oblivion Spiral** in a resounding boom of power that was dead even. Both attackers roared louder as they tried to overpower the other before Kyuubi gave Naruto the edge he needed with a boost of chakra. The result was Naruto's attack blasting through Aerodactyl's and hitting it square in the chest before driving it down into the ground where it lost its remaining energy and resumed its skeleton form.

Growling, Naruto reared his head back and roared victoriously as an influx of power was released from him, kicking up the wind and pushing the others back.

"W-What is he?!" Oakley gasped out as she fell out of the control seat in her fear. Annie didn't answer and was only able to take a step back in fear.

Latios knew something was wrong as he flew over to Naruto and red eyes met pure black. _"Naruto, you have to snap out of it! You're not in control!"_

Naruto responded with an attempted **Night Slash**, but Latios was fast enough to avoid it. The redhead was about to charge before a weak voice stopped him.

_"N-Naruto…"_

His eyes widened as he turned to Latias and she struggled to look at him. He recoiled in fear as he saw her eyes releasing tears; tears that fell for _him_.

_"Come back, Naruto… You control your own power; not the other way around."_

Naruto took another step back before he gasped and gripped his head in agony. Swirling energies of blue, red, black, and purple/orange raged around him as his black pools returned to their normal blue pupils and the energies calmed down enough to flow back into him peacefully. As soon as they did, his eyes rolled back and he fell unconscious.

_"Naruto!"_ Latias cried and, after being freed by the combined efforts of Yurei and Gojira, flew over to him and lifted his head up gently. _"Naruto… Wake up… Please!"_

There was no response, and it frightened her before more tears welled up and she hugged him close. She cradled his head and prayed to Arceus for him to wake up before an unknown voice spoke up.

"Geez kid… I leave you alone for _one_ day and this kind of crap happens?"

Everyone, save for Naruto, turned to see a tall man with long white hair walking calmly inside the museum followed by a green toad-like Pokémon. The human was a tall man with waist-length, spiky white hair usually tied back into a pony tail, with two shoulder-length bangs that framed both sides of his face. He also had red lines that ran down from his black eyes and wore a horned forehead protector with the kanji for "Oil". He also had a noticeable wart on the left side of his nose and wore a green short shirt kimono and matching pants; under which he wore mesh armor that showed out of the sleeves and legs of his outfit. His outfit was completed with hand guards, a simple black belt, wooden sandals, a red haori with two simple yellow circles on each side, and a scroll on his back.

The Pokémon was a green, bipedal, frog-like creature with yellow hands, belly, throat, and toes. It had a long, curled hair on top of its head and pink cheek spots. There was also a green swirl on its belly while its legs looked well developed and it has bulbous toes and fingers.

The man sighed as he quickly knocked out the two thieves with thin needles that stabbed into their neck pressure points. Once that was taken care of, he stepped over to where Latias held Naruto and mentally noted how protectively she held him; not to mention how fiercely she looked at him as if fearing he was going to attack.

"Relax, I'm his teacher. My name is Jiraiya and that kid you're holding is my apprentice, Naruto."

"If you're his teacher, then where were you all this time?!" yelled Bianca in anger. With how easily he took out those women, he could've easily handled the _entire_ situation in her eyes.

"I was meeting up with someone in regards to my responsibilities to the Leaf Village; our home across the ocean," answered the Toad Sage as he hefted Naruto over his shoulder and began to walk out. His Politoed meanwhile used the ninja wire Jiraiya had given him to tie up Annie and Oakley for the authorities. "Good job, Gama," Jiraiya stated as he returned the toad Pokémon to his Pokéball.

The others, seeing the situation finally solved, followed after. However, Latios grabbed the Soul Dew from the machine and sighed in relief at the sight of it still intact and his father's soul still residing in it. He was worried that he'd have to become a _new_ Soul Dew if his father's soul was used up.

Following after the others, he easily noted the worry in Latias' face as she floated next to Naruto's unconscious form and even rubbed her head against his cheek in hopes of waking him. He smiled at how attached she had gotten to him as he thought of what was best for her future.

[Next Morning]

The first thing Naruto noticed when he came to was that he was lying on a soft bed covered in a blanket. The next thing he noticed was that someone was sleeping beside him, and he turned to see that it was Bianca. Or at least, he thought it was Bianca.

Gently nudging her, he saw her eyes flutter open before her sleepy gaze met his. They fully opened when they saw him, and she engulfed him in a tight hug as a flash of light revealed her returning to her natural Pokémon form.

_"Thank Arceus that you're alright!"_ she exclaimed as she hugged him, making him awkwardly return it since he was not used to the affectionate gesture.

"What happened? How did I wind up here? The last thing I remember was seeing you get caught and then getting really pissed off."

She nodded and replied, _"That happened and then you suddenly began to let off a large amount of power. It felt like aura; a power some rare humans can use. However, it also felt like poképower."_

"How did I use poképower when I'm a human?"

_**"****Your chakra coils absorbed it since the air around the museum chamber was practically saturated in the combined energies of chakra and poképower. You gained two new 'pipes' in here as well, brat."**_

_"He's right, Naruto,"_ Latias stated, backing up Kyuubi's statement. _"I can feel two distinct Pokémon energies inside of you."_

"Wait, how did you just here Kyuubi? And why aren't you afraid of me?"

"_I've linked my mind to yours so that I can speak, so I can also hear the Kyuubi speak as well. We actually spoke a bit before we all slipped into exhaustion and he was quite informative about your situation."_

"I…see," he replied in dazed surprise.

"_As for not fearing you… Why would I be afraid of someone who saved my life, saved my brother from being used, saved my home, and kept my father's Soul Dew from being used up?"_ she asked with a smile, making him give a small one in return.

"Thank you…"

She shook her head and stated, _"No, thank _you_ Naruto for everything you've done for me and my brother."_ She then leaned in and kissed his cheek with a small blush while his face resembled a tomato.

When he calmed it down, he looked around the room and saw his two Pokémon resting on the bed next to his. "I'm glad you two are okay," he murmured as he found their Pokéballs on his nightstand and returned them. He then stood up and stretched while Latias took on her disguise of Bianca, making him look at her curiously. "Have you ever thought of going with a different look?"

_"What do you mean?"_ she asked back as she tilted her head in confusion.

"It's just…I can't see you as _you_ if you're disguised as Bianca. I keep thinking that _you're_ Bianca instead of Latias."

She frowned in thought at that and honestly didn't like the idea of Naruto seeing her as Bianca instead of herself. Reverting back to her Pokémon form, she asked, _"What should I do then?"_

"Give yourself a look that represents you as an individual. Personally, I don't like the fact that you have to hide yourself, but I know it's essential. Just imagine yourself as a human, yet still _you_ as a Pokémon."

She hummed in thought before her eyes began to glow pure white and she engulfed her form in a red swirl. It was bright enough to force Naruto to cover his eyes and when the light died down, he gaped at what he saw.

Before him stood a young woman with tan skin, white hair with protrusions that looked like Latias' ears, and amber eyes. On her forehead was an upside-down red triangle while a string necklace with a blue triangle pendant was around her neck. She wore a white shirt and skirt with a red trim, black shorts that hugged her legs and fell to the tops of her knees, red fingerless gloves, and red sandals that looked like his own black ones. (1)

She looked over her form and then looked to him shyly and asked, _"Is this okay?"_

He couldn't help but blush slightly at how beautiful she looked before he rubbed his head with a grin. "I-It's perfect! You look great, Latias!"

She smiled happily before she grabbed his hand and practically dragged him downstairs to where the others were waiting. Latios was resting at their secret garden, so he wasn't there with them.

Misty was the first to notice them and she waved. "Over here you two!"

Naruto and Latias walked over to them and Bianca smiled at the Pokémon's new look. She also hid a giggle at how close she stood next to Naruto and how oblivious he was to it.

"Glad to see that you're alright, Naruto," she stated. "You had everyone worried; especially Latias."

Said Pokémon blushed as Naruto smiled sheepishly. "Yea, sorry to worry you all… I'm just glad that everything was all settled." He then turned to Jiraiya and pointed an accusing finger at him angrily. "Speaking of that; where the hell were you, Pervy Sage?! We could've really used your help!"

"Brat, how many times have I told you not to call me that?!" yelled back the hermit as they both got into each other's faces in a comical way, making the others laugh. When they backed off, Jiraiya explained, "I had to go see someone concerning my role in the village. You know how it is, brat."

Sighing, the redhead nodded. "Yea yea, I know that. But still, we really needed some help."

"Actually, I'd say you did pretty well without me. Sure, you overworked yourself and did something reckless as usual, but you still pulled off saving the city. You've grown from your younger days, and you should be proud of yourself."

Naruto rubbed he head bashfully before he remembered something. "Hey, do you three know about…well, me?" he asked Ash and his friends.

Brock was the one who answered. "Yea, you're teacher told us about where you come from; at least as much as we needed to know. All we know is that you use a power similar to aura, your home country has no known Pokémon, and that you're away on a training trip."

Naruto nodded before Ash stood up with a grin. "Alright, now that that's settled… Let's have out Pokémon Battle! You have two Pokémon now, so we can do a two-on-two!"

"Right now?" questioned the Uzumaki in surprise.

"You'd be better off doing it now since our boat leaves tomorrow and we need to get some supplies for our return trip," informed Jiraiya.

"But I still don't really know how to do a Pokémon battle, let alone what they're capable of," argued the redhead.

The others looked to Ash who sighed in defeat. "We can postpone it for later. The Pokémon Center in town should have what you need in order to learn how to battle."

"Alright, but where's the Center?"

"I'll take you there," Bianca stated as she began walking off. "C'mon, we don't have all day, you know."

He quickly took off after her while Latias looked slightly conflicted, making Jiraiya smirk. _'Oh ho, what do we have here? Is there someone crushing on my godson?'_

It seemed as if she made a decision since she quickly took off after them, making Jiraiya laugh boisterously and walk away, much to the confusion of the others before they decided to follow as well. They had nothing really important to do anyway.

Once they reached the Center, Bianca led Naruto to the pink haired Nurse Joy who was more than happy to give Naruto a paperback version of Professor Oak's Pokédex that covered the regions of Kanto, Johto, Hoenn, and most of Sinnoh. After thanking her for the book, Naruto looked up whatever he could on his two partners and was surprised at how much information each Pokémon had. It showed what they evolved into or from, what moves they learned as they grew, what Pokémon they can have as parental figures (resulting in eggs), and also a basic summary of their habits and diets.

Bianca also found him a book specifically for Pokémon Battles and he found himself growing more and more excited at each turn of the page. By the time he had finished reading everything he could on his Pokémon and on Battling, a little over three hours had passed.

"Okay, I think I've got all I need," exclaimed Naruto as he put the books away into his pouch. Ash couldn't contain his excitement as he led the others outside to one of the practice fields behind the Pokémon Center.

Brock decided to officiate the match and Ash threw out his first Pokémon. It was a small, bipedal Pokémon with bluish fur on top of its body, and a milky color on the underside. It seemed to be a composite of features from the echidna and the shrew. The echidna features were the flames from its back, while its general body shape was shrew-like. Its eyes were squinted closed, much like Brock's, and it has a long, thin snout. Though it lacked claws on its forelimbs, but has a single claw on each hind foot.

"Let's do this, Cyndaquil!" exclaimed Ash excitedly as the Pokémon had the flame spots on its back roar to life.

"Okay then, let's go with Gojira!" Naruto declared as he released said Pokémon from her ball. She growled at Cyndaquil and readied herself for the battle.

As soon as Brock called for them to start, Ash had Cyndaquil start things off with a **Flamethrower**, but Gojira countered after Naruto called for her to use **Sandstorm**. The flurry of sand and dust broke through the fire, but Ash had Cyndaquil move out of the way before attacking with a **Flame Wheel**.

Now a spinning ball of fire, Cyndaquil rolled after Gojira, but Naruto had her brace herself with her arms stretched forward. The result was her forelimbs catching the spinning fireball and being pushed back only slightly before Naruto had her toss Cyndaquil away. The dazed Pokémon was then open for a **Mud Slap** which hit it in the face and blinded it enough for Gojira to fire one last **Sandstorm**. It got a direct hit and Cyndaquil was blasted back and tumbled across the ground before it became knocked out.

"Cyndaquil is unable to battle, so Larvitar is the winner!" Brock called out, making Naruto fist pump at his victory while Gojira smirked proudly.

"Great work, Gojira! Now, take a rest and let Yurei take over."

She nodded and stepped out of the ring before Naruto's Haunter was released and he grinned mischievously. Ash, deciding to see Naruto's best with his own, had Pikachu jump down to battle.

"You ready, buddy?"

"Pika!" the Pokémon exclaimed in excitement.

"Alright, Match Two begins now!" Brock called out.

"Yurei, go for a **Shadow Punch**!" Naruto called out, making the ghost Pokémon grin wider and disappear from sight.

"Keep an ear open, Pikachu, and then use **Iron Tail**."

The mouse-like Pokémon nodded and closed his eyes while his ears twitched every now and then to detect movement. Suddenly, Pikachu spun in place as his tail gained a metallic sheen and he struck out at Yurei, knocking aside its shadowy hand.

"Quick, **Lick** attack!" Naruto ordered and Yurei struck Pikachu with a long and slobbery tongue that dragged up his chin and face, making him gag at the feeling. "Now use **Shadow Ball**!"

"Counter it with a **Thunderbolt**!"

The two Pokémon called upon their respective poképower before a streak of electricity and a sphere of shadowy energy shot at one another and met in the middle with an explosion of smoke. It was thick enough so that none of the Pokémon could be seen, and Naruto couldn't help but grin at being reminded of Zabuza Momochi's **Hidden Mist Jutsu**.

"Yurei, hide in the smoke and keep quiet!"

Not able to see a response and not hearing anything, he assumed that his Pokémon listened to him and waited for the smoke to clear. When it did, Pikachu stood alone on all fours with electric power sparking along his red cheek pouches. He then looked to Ash who had a smile on his face, making him grow worried.

_'Looks like he has a plan already,'_ he thought to himself. _'Maybe if Yurei came from beneath the ground...'_

No sooner did he think that did Pikachu suddenly strike the ground with an **Iron Tail**, easily breaking into the concrete and revealing the hiding Haunter. It desperately made a **Shadow Punch** to keep from being struck, but then Ash called out for something both crazy and brilliant.

"Mix electricity into your tail, Pikachu!"

The resulting maneuver had Pikachu's **Iron Tail** infused with a strong electric current that not only broke through the **Shadow Punch**, but also struck the ghost Pokémon in the face and knocked it out in a clean shot.

"Haunter is unable to battle, so Pikachu wins and this match is a draw!" Brock called out as Naruto returned his Pokémon and Pikachu returned to Ash's shoulder.

As they shook hands, the redhead stated, "Not bad, Ash. I never thought you'd mix moves like that."

"It just came to me, really," Ash explained sheepishly.

"Well, it was still a good battle. Plus, it's shown me that I can mix my Pokémon's moves as well!"

Off to the side, Misty and Bianca clapped at the battle while Latias simply smiled at the sight of the happy trainers. However, her smile fell when she realized that Naruto was set to leave tomorrow. She felt a strange empty feeling at the thought of him leaving, and it confused her.

She would need to speak to her brother about this.

[The Next Day (Docks)]

Naruto watched on with slight sadness at the sight of the boat meant to take him and his perverted teacher back home. He had seen so much, met some amazing creatures and people, and gained some cool friends all in the span of a couple of days and now he'd be returning to the "normalcy" of being a shinobi.

He turned back to the city and saw his friends standing there to see him off. It made him smile at the sight while unconsciously thinking of how no one was there to see him off when he left home.

_'I wonder how different my life would be if I was born in this part of the world,'_ he mused as he walked over to them.

"Shoving off, huh?" Misty asked which Naruto nodded to. She gave him a farewell hug and said, "It was great to meet you. Maybe we'll meet again someday."

"Yea, and when we do, we'll have another battle," Ash exclaimed as he shook Naruto's hand.

"I'll look forward to it," replied the whiskered shinobi.

"Take care of yourself, and here; take this," Brock said before handing him a book on breeding. "It should help in raising you Pokémon as well as little tips for their food and other things."

"Thanks Brock. This means a lot to me."

Bianca then stepped up and handed him a small frame and he turned it around to see a painting of himself with Gojira standing in front of him while Yurei, as a Gastly, rested in his hair.

"I figured you'd like that for sentimental reasons," she explained before she hugged him. "Take good care of them, Naruto."

"I will, and thanks for this," he said before he headed to the ship and stepped aboard beside Jiraiya.

Noticing his downcast look, he asked, "Missing them already, even though we haven't left?"

"I can't help it if I do, Pervy Sage. There was just so much amazing things here, and now we're leaving it all when I only had a taste of it. Plus…"

He left the last part hanging as he tried to locate Latios or Latias, but he didn't see them. Sighing, he went to the lower decks as the ship set sail away from Altomare's docks. Jiraiya frowned sadly at his godson's depressed aura, but there wasn't anything he could do since they were both needed back home. Turning back, he gave a small wave to the distancing people Naruto had befriended before he went below as well.

Meanwhile, back on the docks, Latios and Latias watched the ship leave with their down feathers hiding them from view. The blue eon looked to his sister and saw that she was watching the ship leave with a conflicted expression.

_"You know, I've been thinking over some things lately; mainly with how I've helped raise you,"_ he began, making her turn to him. _"I think that you'd have a much better experience in life if you left the city and saw the world beyond the blue waters."_

_"But...what about you and this city? They need us to watch over them, right?"_ she asked softly.

_"True, but I'm sure I can take care of things with Bianca and Lorenzo. Besides, I'll always have father here with me. My place is here, sister. Yours,"_ he started before he nodded to the ship on the horizon, _"is out there. It's your decision, but I just want you to know that you have my blessing."_

She turned back to the ship and watched it as she thought over her choices. After some minutes of silent deliberation, she turned back to her smiling older brother and embraced him. _"I'll miss you, brother."_

_"I'll miss you as well, dear sister. Now, go on before you lose him,"_ he said in a teasing tone that made her blush before she smiled brightly and shot off across the water like a rocket. As he watched her go, his smile softened as he murmured out to the horizon, _"Take care of her, Naruto… And Lord Arceus, please watch over her."_

**(End Chapter)**

1~ The link to how Latias (Akarei) looks for the remainder of this story is on my profile

So, what did you guys think of the second chapter? I hope it turned out well and made you all eager for more!

Reminder Note from Above: Naruto won't be involved with anyone else but Latias (Akarei) while Mew will become an eventual sister figure to him!

Now, I'm sure you guys have plenty of questions or concerns. If you do and would like them answered, please PM them to me and I will get back to you as soon as possible! Also, be sure to review this story guys! Please and thank you!

Next Time: A dragon joins Naruto as he returns home after three years abroad! What will she think of the Leaf Village?! Stay Tuned!

**pain17ification**


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